The DNA of all organisms is constantly under attack by both endogenous and exogenous agents. If unrepaired, the resulting DNA lesions can miscode (mutagenic effects), or alter the specificity of DNA-protein interactions (epigenetic effects). Both mutational events and epigenetic perturbations resulting from DNA damage have been identified in human cancer. Substantial work from many laboratories has identified an array of DNA lesions as well as specific repair activities that recognize and remove these lesions. It is now widely recognized that individuals with defects in certain DNA repair pathways are predisposed to develop specific forms of cancer. Cancer susceptibility in genetically normal individuals is likely related to the relative rates of DNA damage and DNA repair. Under normal conditions, it is estimated that between 104 and 105 lesions are formed per cell per day. While this represents a large lesion load, the problem is substantially more complicated because the lesions are dispersed among the 109 normal bases in the human genome. The overall goal of the work described in this proposal is to probe the mechanisms by which lesions are found, identified, selectively removed and repaired through a group of linked experimental and computational studies involving hybrid quantum mechanical and molecular mechanical methods. The focus of this proposal is on single-base lesions repaired by the base excision-repair (BER) pathway. Three specific aims are proposed to investigate (aim 1) the thermal and thermodynamic instability of oligonucleotide regions containing lesions as a mechanism of lesion identification, (aim 2) size, electronic-inductive properties and functional groups of substituents of modified bases that can be exploited for the selective removal of damaged bases, and (aim 3) conformational and dynamic properties of nucleic acids that can be exploited by DNA ligase to prevent the ligation of DNA strands with damaged, inappropriate or mispaired bases. The results of the studies proposed here will substantially increase our understanding of mechanisms that protect the human genome from disease-causing damage and provide new insights into the mechanisms of some antitumor agents. [unreadable] [unreadable]